Starting phenix.real_space_refine on Mon Feb 10 21:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo3_33335/02_2025/7xo3_33335.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1626 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.57, per 1000 atoms: 0.60 Number of scatterers: 2598 At special positions: 0 Unit cell: (79.5, 117.66, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 522 8.00 N 450 7.00 C 1626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 350.5 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 42 removed outlier: 6.386A pdb=" N LEU B 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY E 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 57 removed outlier: 6.293A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 61 through 67 removed outlier: 6.057A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 71 through 72 removed outlier: 6.466A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 75 through 79 removed outlier: 5.994A pdb=" N THR B 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.362A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.898A pdb=" N SER B 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 42 removed outlier: 6.433A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY C 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 57 removed outlier: 8.988A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ALA C 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 67 removed outlier: 6.050A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.445A pdb=" N VAL A 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.033A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.374A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.889A pdb=" N SER A 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) 43 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.35: 407 1.35 - 1.42: 103 1.42 - 1.48: 426 1.48 - 1.55: 1218 Bond restraints: 2610 Sorted by residual: bond pdb=" C GLY B 67 " pdb=" O GLY B 67 " ideal model delta sigma weight residual 1.233 1.227 0.006 6.90e-03 2.10e+04 7.30e-01 bond pdb=" C GLY E 67 " pdb=" O GLY E 67 " ideal model delta sigma weight residual 1.233 1.227 0.006 6.90e-03 2.10e+04 6.58e-01 bond pdb=" C GLY C 67 " pdb=" O GLY C 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 6.26e-01 bond pdb=" C GLY A 67 " pdb=" O GLY A 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 6.24e-01 bond pdb=" C GLY D 67 " pdb=" O GLY D 67 " ideal model delta sigma weight residual 1.233 1.227 0.005 6.90e-03 2.10e+04 5.82e-01 ... (remaining 2605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.36: 2602 0.36 - 0.72: 604 0.72 - 1.08: 232 1.08 - 1.44: 54 1.44 - 1.80: 36 Bond angle restraints: 3528 Sorted by residual: angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N ALA C 85 " ideal model delta sigma weight residual 115.25 116.89 -1.64 1.43e+00 4.89e-01 1.31e+00 angle pdb=" CA GLY B 84 " pdb=" C GLY B 84 " pdb=" N ALA B 85 " ideal model delta sigma weight residual 115.25 116.86 -1.61 1.43e+00 4.89e-01 1.27e+00 angle pdb=" CA GLY F 84 " pdb=" C GLY F 84 " pdb=" N ALA F 85 " ideal model delta sigma weight residual 115.25 116.85 -1.60 1.43e+00 4.89e-01 1.25e+00 angle pdb=" CA GLY D 84 " pdb=" C GLY D 84 " pdb=" N ALA D 85 " ideal model delta sigma weight residual 115.25 116.84 -1.59 1.43e+00 4.89e-01 1.23e+00 angle pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " ideal model delta sigma weight residual 115.25 116.83 -1.58 1.43e+00 4.89e-01 1.22e+00 ... (remaining 3523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.58: 1314 10.58 - 21.16: 128 21.16 - 31.74: 46 31.74 - 42.32: 12 42.32 - 52.90: 18 Dihedral angle restraints: 1518 sinusoidal: 504 harmonic: 1014 Sorted by residual: dihedral pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.66 40.34 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 224 0.026 - 0.051: 118 0.051 - 0.077: 48 0.077 - 0.103: 20 0.103 - 0.129: 52 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 68 " 0.002 2.00e-02 2.50e+03 4.77e-03 2.28e-01 pdb=" C GLY A 68 " -0.008 2.00e-02 2.50e+03 pdb=" O GLY A 68 " 0.003 2.00e-02 2.50e+03 pdb=" N ALA A 69 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 68 " 0.002 2.00e-02 2.50e+03 4.74e-03 2.25e-01 pdb=" C GLY D 68 " -0.008 2.00e-02 2.50e+03 pdb=" O GLY D 68 " 0.003 2.00e-02 2.50e+03 pdb=" N ALA D 69 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 68 " -0.002 2.00e-02 2.50e+03 4.73e-03 2.24e-01 pdb=" C GLY B 68 " 0.008 2.00e-02 2.50e+03 pdb=" O GLY B 68 " -0.003 2.00e-02 2.50e+03 pdb=" N ALA B 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 223 2.76 - 3.29: 2264 3.29 - 3.83: 3987 3.83 - 4.36: 4368 4.36 - 4.90: 8731 Nonbonded interactions: 19573 Sorted by model distance: nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.223 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.223 3.120 ... (remaining 19568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2610 Z= 0.125 Angle : 0.408 1.796 3528 Z= 0.248 Chirality : 0.051 0.129 462 Planarity : 0.001 0.005 438 Dihedral : 12.373 52.896 882 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.007 0.002 PHE F 94 TYR 0.001 0.000 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.304 Fit side-chains REVERT: A 62 GLN cc_start: 0.8271 (tp40) cc_final: 0.8049 (tm130) REVERT: F 97 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6193 (tptt) REVERT: D 97 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6372 (tppt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.6825 time to fit residues: 83.9343 Evaluate side-chains 28 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111704 restraints weight = 3580.772| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.86 r_work: 0.3629 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2610 Z= 0.402 Angle : 0.586 5.138 3528 Z= 0.337 Chirality : 0.055 0.140 462 Planarity : 0.003 0.010 438 Dihedral : 5.731 15.862 378 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.03 % Favored : 84.97 % Rotamer: Outliers : 1.52 % Allowed : 15.91 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.013 0.003 PHE A 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.298 Fit side-chains REVERT: C 62 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: F 60 LYS cc_start: 0.7409 (mtpt) cc_final: 0.7207 (mttm) REVERT: F 97 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6296 (tptt) REVERT: D 97 LYS cc_start: 0.7094 (ttmt) cc_final: 0.6352 (tppt) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.6112 time to fit residues: 59.2159 Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.133544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112915 restraints weight = 3611.754| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.02 r_work: 0.3655 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2610 Z= 0.271 Angle : 0.528 4.680 3528 Z= 0.304 Chirality : 0.052 0.137 462 Planarity : 0.002 0.007 438 Dihedral : 5.461 16.352 378 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.27 % Allowed : 17.80 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.008 0.002 PHE A 94 TYR 0.005 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.277 Fit side-chains REVERT: F 97 LYS cc_start: 0.7187 (ttmt) cc_final: 0.6279 (tptt) REVERT: D 61 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: D 97 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6317 (tppt) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 1.6904 time to fit residues: 53.5117 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.132829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112010 restraints weight = 3630.220| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.00 r_work: 0.3643 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2610 Z= 0.317 Angle : 0.551 4.651 3528 Z= 0.318 Chirality : 0.053 0.137 462 Planarity : 0.002 0.008 438 Dihedral : 5.668 17.333 378 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 2.27 % Allowed : 19.32 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.010 0.003 PHE D 94 TYR 0.006 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.267 Fit side-chains REVERT: F 97 LYS cc_start: 0.7165 (ttmt) cc_final: 0.6271 (tptt) REVERT: D 97 LYS cc_start: 0.7060 (ttmt) cc_final: 0.6287 (tptt) outliers start: 6 outliers final: 5 residues processed: 31 average time/residue: 1.7071 time to fit residues: 53.9727 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.132383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111388 restraints weight = 3598.088| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.01 r_work: 0.3636 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2610 Z= 0.391 Angle : 0.613 5.070 3528 Z= 0.355 Chirality : 0.055 0.140 462 Planarity : 0.003 0.009 438 Dihedral : 5.955 17.986 378 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 1.89 % Allowed : 20.45 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.012 0.003 PHE D 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.334 Fit side-chains REVERT: E 97 LYS cc_start: 0.7578 (ttmt) cc_final: 0.6878 (tmtm) REVERT: F 97 LYS cc_start: 0.7147 (ttmt) cc_final: 0.6263 (tptt) REVERT: D 97 LYS cc_start: 0.7062 (ttmt) cc_final: 0.6289 (tptt) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 1.5781 time to fit residues: 46.7939 Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.133549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112432 restraints weight = 3682.626| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.04 r_work: 0.3651 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2610 Z= 0.317 Angle : 0.562 4.579 3528 Z= 0.324 Chirality : 0.053 0.140 462 Planarity : 0.002 0.008 438 Dihedral : 5.794 17.794 378 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 3.03 % Allowed : 19.32 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.009 0.003 PHE F 94 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.304 Fit side-chains REVERT: F 97 LYS cc_start: 0.7142 (ttmt) cc_final: 0.6252 (tptt) REVERT: D 97 LYS cc_start: 0.7043 (ttmt) cc_final: 0.6283 (tptt) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 1.5272 time to fit residues: 48.5172 Evaluate side-chains 31 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112434 restraints weight = 3656.488| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.04 r_work: 0.3652 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2610 Z= 0.312 Angle : 0.561 4.598 3528 Z= 0.323 Chirality : 0.053 0.142 462 Planarity : 0.002 0.007 438 Dihedral : 5.807 17.862 378 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 3.41 % Allowed : 18.94 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.010 0.003 PHE D 94 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.304 Fit side-chains REVERT: F 97 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6250 (tptt) REVERT: D 97 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6294 (tptt) outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 1.4810 time to fit residues: 50.0073 Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 0.0010 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117555 restraints weight = 3603.261| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.05 r_work: 0.3715 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2610 Z= 0.136 Angle : 0.449 3.752 3528 Z= 0.259 Chirality : 0.052 0.141 462 Planarity : 0.001 0.005 438 Dihedral : 5.006 15.487 378 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.27 % Allowed : 20.45 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE F 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.300 Fit side-chains REVERT: F 97 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6291 (tptt) REVERT: D 97 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6224 (tptt) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 1.5571 time to fit residues: 50.9965 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.132499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111446 restraints weight = 3621.796| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.99 r_work: 0.3637 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2610 Z= 0.392 Angle : 0.597 4.629 3528 Z= 0.344 Chirality : 0.055 0.143 462 Planarity : 0.003 0.010 438 Dihedral : 5.918 18.461 378 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.03 % Favored : 84.97 % Rotamer: Outliers : 2.27 % Allowed : 20.08 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.012 0.003 PHE D 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.282 Fit side-chains REVERT: F 97 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6092 (tptt) REVERT: D 97 LYS cc_start: 0.7068 (ttmt) cc_final: 0.6287 (tptt) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 1.5810 time to fit residues: 56.5117 Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120429 restraints weight = 3564.553| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.04 r_work: 0.3759 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2610 Z= 0.121 Angle : 0.456 4.445 3528 Z= 0.260 Chirality : 0.052 0.144 462 Planarity : 0.001 0.005 438 Dihedral : 4.764 14.462 378 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.89 % Allowed : 20.83 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 50 PHE 0.004 0.001 PHE E 94 TYR 0.003 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.299 Fit side-chains REVERT: F 97 LYS cc_start: 0.6955 (ttmt) cc_final: 0.6126 (tptt) REVERT: D 97 LYS cc_start: 0.6969 (ttmt) cc_final: 0.6207 (tptt) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 1.5025 time to fit residues: 44.6107 Evaluate side-chains 29 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.0060 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 3.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.133057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.112143 restraints weight = 3667.690| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.01 r_work: 0.3640 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2610 Z= 0.330 Angle : 0.563 4.384 3528 Z= 0.323 Chirality : 0.054 0.145 462 Planarity : 0.002 0.007 438 Dihedral : 5.693 18.009 378 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 1.89 % Allowed : 20.83 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.010 0.003 PHE D 94 TYR 0.006 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.03 seconds wall clock time: 42 minutes 15.85 seconds (2535.85 seconds total)